2O40

Crystal Structure of a Chemically Synthesized 203 Amino Acid 'Covalent Dimer' HIV-1 Protease Molecule

• PDB DOI: https://doi.org/10.2210/pdb2O40/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Human immunodeficiency virus type 1
• Mutation(s): No 


• Deposited: 2006-12-02 Released: 2006-12-19 
• Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Convergent chemical synthesis and crystal structure of a 203 amino acid "covalent dimer" HIV-1 protease enzyme molecule.

Torbeev, V.Y., Kent, S.B.

(2007) Angew Chem Int Ed Engl 46: 1667-1670

• PubMed: 17397076 
• DOI: https://doi.org/10.1002/anie.200604087
• Primary Citation of Related Structures:  
  2O40

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Organizational Affiliation: 

Department of Chemistry, Institute for Biophysical Dynamics, Gordon Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.66 kDa 
• Atom Count: 1,654 
• Modelled Residue Count: 203 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
covalent dimer HIV-1 protease	A	203	N/A	Mutation(s): 0  EC: 3.4.23.16
UniProt
Find proteins for O38716 (Human immunodeficiency virus type 1) Explore O38716  Go to UniProtKB:  O38716

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2NC	B [auth A]	N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide C35 H68 N11 O8 MQPXOVRKKPPKFZ-QYKDHROSSA-O

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
NLE	A	L-PEPTIDE LINKING	C6 H13 N O2		LEU
YCM	A	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000398 (2NC)	B [auth A]	N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.326	α = 90
b = 58.306	β = 90
c = 61.699	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2013-02-27
  Changes: Other
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Derived calculations